virus 3

IntroductionTitle: Viruses Structure and EntryInstructor: Prof. Moshe Dessau (Contact: moshe.dessau@biu.ac.il)Location: Udessaum particinoll

This set of notes provides a comprehensive overview of viral classification, structure, and the mechanisms through which viruses infect host cells. It covers different types of viruses, including Herpesvirus, Atomic virus, Flexuous tailed phages, and Tubulovirus, which represent a diverse range of viral morphologies and genetic material. Understanding these classifications is essential for studying virus biology and the development of antiviral therapies.

The principles of virus structure emphasize critical functions such as genome protection and delivery. This section discusses how the viral capsid or envelope is vital in safeguarding the nucleic acid while facilitating attachment to host cells. Protein-protein interactions are also highlighted for their role in the construction of viral structures, where the interactions between different viral proteins influence the overall shape and stability of the virion.

To study virus structure, X-ray crystallography is a primary method utilized by virologists. This technique involves several key components, including film diffraction, where x-rays are directed at a crystallized sample to observe the patterns formed by scattered rays. Data collection and phasing are critical steps, allowing scientists to understand the arrangement of atoms within the crystal. Model building and refinement further enhance the accuracy of the resulting three-dimensional structures derived from the crystallographic data. Significant insights from these studies include the maximum and mean radius measurements of viral structures, with historical references noting the pioneering work of Rosalind Franklin in 1956, and earlier contributions by Barnel and FanKuchen in 1937.

Icosahedral symmetry is another critical concept in structural virology, demonstrated by Donal Caspar in 1956 when observing Tomato Bushy Stunt Virus (TBSV) through an X-ray study. This type of symmetry is common among viruses, offering a framework for a stable and efficient virion structure. In addition, Cryo-electron microscopy (CryoEM) represents a modern technique that allows for high-resolution imaging of viruses in a near-native state. This method involves scanning micrographs that prevent radiation damage to the specimen, utilizing Fourier transform techniques to analyze the orientation of particles. Key steps include merging transforms, refining the data, and reconstructing three-dimensional high-resolution images of viral structures.

When focusing on specific viruses, the Zika virus exemplifies current research interests in enveloped viruses. Described as an enveloped, single-stranded RNA (+) virus, the Zika virus is characterized by unique motifs and its assembly intermediates in the infected host. An illustrative example is provided with the dsRNA phage ϕ6, which shows how assembly involves a scaffold protein shell, shedding light on the complexities of viral assembly processes.

Virions can be classified into non-enveloped and enveloped categories. Non-enveloped viruses consist of a protective capsid surrounding their genetic material (either DNA or RNA) while enveloped viruses possess an outer lipid bilayer that contains embedded glycoproteins, forming a ribonucleoprotein (RNP) complex. Understanding these structural differences is pivotal for vaccine and therapeutic developments, particularly concerning how viruses interact with host cell membranes.

A comparative analysis illustrates the structural components between viruses. For instance, the herpes simplex virus type I (HSV-I) is enveloped with double-stranded DNA, contrasted with the Influenza virus, which possesses an envelope with single-stranded RNA (+). This understanding leads into a discussion of the phylogenetic tree of viral lineages, presenting a structural comparison that illustrates four major viral lineages based on capsid protein structures, including Picorna-like, HK97-like, PRD1/adeno-like, and BTV-like viruses.

Symmetry plays a fundamental role in biology and is observed in many molecular structures, including viruses. It contributes to the stability and functional efficiency of biological macromolecules, thus enabling proper biological activity and fitness. Discussions on symmetry operations encompass various transformations affecting geometric objects, including translation, reflection, and rotation. Visual examples are provided to illustrate 2-fold rotational symmetry. Furthermore, the notes delve into the intricacies of rotational symmetry operations, classifying them into types such as twofold (180°), fourfold (90°), and threefold (120°).

The document explains translation symmetry, a vital concept in geometric structures, and introduces screw symmetry operations, which reflect a combination of rotation and translation leading to complex symmetrical patterns. Understanding these symmetries is key for researchers looking to manipulate or replicate viral structures in laboratory settings.

Helical symmetry specific to viruses is demonstrated through axial measurements of the Tobacco Mosaic Virus and Vesicular Stomatitis Virus. The significance of ribonucleoproteins within the Influenza virus is also examined, characterizing their structure and denoting their importance in the overall composition and function of the virus. Furthermore, the icosahedral assembly of viruses indicates how symmetrical structures can accommodate complex viral genomes effectively, highlighting various structural axes that are crucial during viral assembly and infection.

An analysis of structural organization within capsids discusses the distinctions of several types, particularly emphasizing triangulation through T-number classifications are given (T=1, T=3, T=4, T=13), showcasing how triangular modules contribute to capsid formation. The Poliovirus is then discussed in detail, noted for being non-enveloped with an approximate diameter of 30 nm and a genome of about 7.5 kb ssRNA(+).

This document contains visual aids exemplifying asymmetric capsid assembly seen in retroviruses, illustrating unique structural forms and the importance of specific viral proteins in the assembly process. An exploration of enveloped viruses details components of the influenza virus, identifying entrenched glycoproteins and membrane structures while exploring the dynamic nature of viral envelopes, with a specific focus on how the dengue virus undergoes structural changes at varying temperatures, offering insights into viral adaptability.

The pleomorphic nature of viruses such as Influenza and Hanta viruses, categorized as enveloped ssRNA viruses, highlights their variable shapes and structural flexibility. This flexibility may contribute to their functionality and efficiency in infecting host cells, as well as their ability to evade immune responses.

In examining complex virus assembly, an overview of Herpes simplex virus 1 (HSV-1) is provided, detailing its structural composition, including both capsid and envelope components that are vital for its infective capabilities. The underlying principles of virus attachment and entry into host cells are dissected, addressing various strategies that viruses employ to bind to cellular receptors and penetrate cellular membranes.

The document presents key receptors and co-receptors, such as CD4 and Heparan sulfate proteoglycan, essential for facilitating viral entry into host cells. Experimental approaches to identifying these viral receptors are outlined, focusing on the techniques utilized to discern permissive cells that allow for successful viral entry and replication. Additionally, an extensive compendium of specific receptors for various virus particles provides insights into their mechanisms of infection, including those for HIV-1 and herpes simplex virus.

Mechanisms of macromolecule uptake by cells such as phagocytosis and endocytosis are explored thoroughly as they relate to viral entry. These processes serve as crucial pathways for viruses to gain access to the interior of host cells, where they can replicate and propagate. Furthermore, entry routes for viruses are explored, examining both clathrin-dependent and caveolin-independent pathways, emphasizing their significance in the infection process.

Uncoating mechanisms are detailed, explaining how viral uncoating varies at different cellular sites, contingent on the type of virus involved, and discussing specific methods of uncoating for both enveloped and non-enveloped viruses.

Energy considerations related to membrane fusion during viral entry are analyzed. This section particularly focuses on the energetic barriers and molecular interactions crucial for successful membrane fusion to occur. Classification of viral membrane fusion proteins based on their structure and function leads into a discussion on Classes I, II, and III fusion proteins that span across diverse viral families. These classifications are pivotal for understanding how different viruses gain entry into host cells.

The document also covers the intricate mechanics of viral proteins, focusing on the hemagglutinin (HA) protein during the fusion process of the influenza virus. Insights are provided regarding the pre- and post-fusion conformational changes of dengue virus proteins, elucidating how such transformations facilitate membrane fusion and effective viral entry. Lastly, an overview of Class III membrane fusion proteins illustrates their structures and functions, followed by a detailed discussion regarding vesicular stomatitis virus (VSV) glycoproteins as exemplary Class III proteins that highlight the versatility of viral fusion mechanisms.